The Biochemistry of Drug Metabolism – An Introduction

This review is part of a series of review articles on the metabolism of drugs and other xenobiotics published in Chemistry & Biodiversity. After a thorough discussion of metabolic reactions and their enzymes, this article focuses on genetically determined differences in drug and xenobiotic metabolism. After a short introduction on the causes for genetic differences, the first focus is on species differences in drug and xenobiotic metabolism. A major chapter is then dedicated to clinically relevant genetic polymorphisms in human drug metabolism and resultant ethnic differences. The last two chapters deal with sex‐dependent differences in drug metabolism and personalized pharmacotherapy related to inter‐individual differences in drug metabolism.     

The Biochemistry of Drug Metabolism – An Introduction

This review continues a general presentation of the metabolism of drugs and other xenobiotics begun in three recent issues of Chemistry & Biodiversity. The present Part is dedicated to reactions of conjugation, namely methylation, sulfonation, and phosphorylation, glucuronidation and other glycosidations, acetylation and other acylations, the formation and fate of coenzyme A conjugates, glutathione conjugation, and the reaction of amines with carbonyl compounds. It presents the many transferases involved, their nomenclature, relevant biochemical properties, catalytic mechanisms, and the reactions they catalyze. Nonenzymatic reactions, mainly of glutathione conjugation, also receive due attention. A number of medicinally, environmentally, and toxicologically relevant examples are presented and discussed.     

细胞色素P450基因多态性与药物代谢研究进展

细胞色素P450（cytochrome P450,CYP450）在人体药物代谢过程中起着非常重要的作用并参与代谢80%以上的临床药物。由于CYP450在不同种族和不同人群中存在基因多态性,从而造成药物反应的个体差异,一度成为药物基因组学研究的热点。通过查阅国外相关文献,综述了近年来关于CYP1A2、CYP2C9、CYP2C19、CYP2D6和CYP3A4五种主要的药物代谢酶的基因多态性和药物代谢的研究进展,为临床指导个体化用药、避免药物不良反应和新药研发提供科学参考依据。     

Modelling the pharmacokinetics of tramadol: on the difference between CYP2D6 extensive and poor metabolizers

In this work we propose a mathematical model for the kinetics of tramadol, a synthetic opioid commonly used for treating moderate to severe pain. This novel theoretical framework could result in an objective criterion on how to adjust the assigned dose, depending on the genetic polymorphisms of CYP2D6. The model describes the coupled dynamics of tramadol and the metabolite O-desmethyltramadol. The effect of diffusion of the drug in the blood is here accounted for and we further hypothesize the existence of a time delay in the process of chemical translation from tramadol into metabolites. The system of coupled differential equations is solved numerically and the free parameters adjusted so to interpolate the experimental time series for the intravenous injection setting. Theoretical curves are shown to reproduce correctly the experimental profiles obtained from clinical trials. This enables in turn to extract an estimate of the metabolization rate. A difference in metabolization rate between CYP2D6 poor and extensive metabolizers is also found, and the stereoselectivity in the O-demethylation of tramadol highlighted. Our results allow one to quantify the dose of (+)-tramadol (resp. (-)-tramadol) administered to poor or extensive metabolizers, if the same effect is sought. The latter is here quantified through the blood concentration of (+)-metabolites (resp. (-)-metabolites).     

Metabolism of the mesoionic compound (MI‐D) by mouse liver microsome,detection of its metabolite In Vivo,and acute toxicity in mice

The mesoionic derivative 4‐phenyl‐5‐[4‐nitrocinnamoyl]‐1,3,4‐thiadiazolyl‐2‐phenylamine chloride (MI‐D) has antitumoral and anti‐inflammatory effects. In this study, we present aspects of its metabolism and toxicity in mice. MI‐D was metabolized in vitro by liver microsome, generating a main product with a much shorter retention time than MI‐D in high‐performance liquid chromatography (HPLC) analysis but with a spectrum similar to that of the original molecule. Mass spectrometry with electrospray ionization in positive mode analysis of the purified compound by HPLC indicated that the product of metabolism has four additional hydroxyl groups (m/z = 465) compared with MI‐D (m/z = 401). The HPLC analyses of plasma and urine samples from mice treated with MI‐D showed the presence of the metabolite product. The kinetic parameters K_m (19.5 ± 4.5 μM) and V_max [1.5 ± 0.4 units of fluorescence/(100 μg of microsomal protein/mL/s)] were estimated, confirming the metabolism of MI‐D and indicating that the reaction follows Michaelis‐Menten kinetics. Acute toxicity was established on the basis of an estimation of mean lethal dose (LD‐50; 181.2 mg/kg) and histopathological analysis of animals that survived the LD‐50 test. Abdominal adhesions, inflammatory foci, and formation of granulomas were observed. Altogether, the results contribute to the advancement of research in support of MI‐D as a future chemotherapeutic drug. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:394–405, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20303     

π–π Stacking mediated drug–drug interactions in human CYP2E1

Because of having many low molecular mass substrates, CYP2E1 is of particular interests to the pharmaceutical industry. Many evidences showed that this enzyme can adopt multiple substrates to significantly reduce the oxidation rate of the substrates. The detailed mechanism for this observation is still unclear. In the current study, we employed GPU‐accelerated molecular dynamics simulations to study the multiple‐binding mode of human CYP2E1, with an aim of offering a mechanistic explanation for the unexplained multiple‐substrate binding. Our results showed that Thr303 and Phe478 were key factors for the substrate recognition and multiple‐substrate binding. The former can form a significant hydrogen bond to recognize and position the substrate in the productive binding orientation in the active site. The latter acted as a mediator for the substrate communications via π–π stacking interactions. In the multiple‐binding mode, the aforementioned π–π stacking interactions formed by the aromatic rings of both substrates and Phe478 drove the first substrate far away from the catalytic center, orienting in an additional binding position and going against the substrate metabolism. All these findings could give atomic insights into the detailed mechanism for the multiple‐substrate binding in human CYP2E1, providing useful information for the drug metabolism mechanism and personalized use of clinical drugs. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

皂苷类药物代谢实验方法研究进展

许多皂苷类天然产物具有医疗保健作用。本文主要从皂苷药代体内外研究方法、皂苷药代生物样品预处理方法和检测方法等方面,概述了皂苷成分药物代谢实验方法的研究进展情况。     

An Urban Metabolism and Carbon Footprint Analysis of the Jing–Jin–Ji Regional Agglomeration

Urban energy metabolism includes processes for exploiting, transforming, and consuming energy, as well as processes for recycling by‐products and wastes. Embodied energy is the energy consumed during all of these activities, both directly and indirectly. Multiregional input‐output (MRIO) analysis can calculate the energy consumption embodied in flows among sectors for multiple cities or regions. Our goal was to address a problem apparent in previous research, which was insufficient attention to indirect energy flows. We combined MRIO analysis with ecological network analysis to calculate the embodied energy consumption and the energy‐related carbon footprints of five sectors in three regions that comprise the Jing‐Jin‐Ji agglomeration, using data from 2002 and 2007. Our analysis traced metabolic processes of sectors from the perspective of final consumption. Based on the embodied energy analysis, we quantified the indirect energy consumption implied in exchanges of sectors and its distribution and identified the relationships formed through the indirect consumption to analyze the roles of providers and receivers in the system. Results showed that the embodied energy consumption for the Jing‐Jin‐Ji region increased from 2002 to 2007 as a result of increased energy consumption in Tianjin and Hebei. Overall, consumption of Beijing decreased likely attributable to the fact that government policies relocated industries during this time in anticipation of the Olympic Games. The relationships among sectors changed: Beijing changed from a net exporter to an importer, whereas Hebei changed from a net importer of energy from Beijing to an exporter to Beijing, and Tianjin served as an importer in both years.     

Pharmacogenomics of Drug Metabolizing Enzymes and Transporters:Relevance to Precision Medicine

The interindividual genetic variations in drug metabolizing enzymes and transporters influence the efficacy and toxicity of numerous drugs. As a fundamental element in precision med-icine, pharmacogenomics, the study of responses of individuals to medication based on their genomic information, enables the evaluation of some specific genetic variants responsible for an individual’s particular drug response. In this article, we review the contributions of genetic polymorphisms to major individual variations in drug pharmacotherapy, focusing specifically on the pharmacoge-nomics of phase-I drug metabolizing enzymes and transporters. Substantial frequency differences in key variants of drug metabolizing enzymes and transporters, as well as their possible functional consequences, have also been discussed across geographic regions. The current effort illustrates the common presence of variability in drug responses among individuals and across all geographic regions. This information will aid health-care professionals in prescribing the most appropriate treatment aimed at achieving the best possible beneficial outcomes while avoiding unwanted effects for a particular patient.     

Albumin Supplement Affects the Metabolism and Metabolism‐Related Drug–Drug Interaction of Fenoprofen Enantiomers

The influence of albumin towards the metabolism behavior of fenoprofen enantiomers and relevant drug–drug interaction was investigated in the present study. The metabolic behavior of fenoprofen enantiomers was compared in a phase II metabolic incubation system with and without bovine serum albumin (BSA). BSA supplement increased the binding affinity parameter (Km) of (R)‐fenoprofen towards human liver microsomes (HLMs) from 148.3 to 214.4 μM. In contrast, BSA supplement decreased the Km of (S)‐fenoprofen towards HLMs from 218.2 to 123.5 μM. For maximum reaction velocity (Vmax), the addition of BSA increased the Vmax of (R)‐fenoprofen from 1.3 to 1.6 nmol/min/mg protein. In the contrast, BSA supplement decreased the Vmax value from 3.3 to 1.5 nmol/min/mg protein. Andrographolide–fenoprofen interaction was used as an example to investigate the influence of BSA supplement towards fenoprofen‐relevant drug–drug interaction. The addition of 0.2% BSA in the incubation system significantly decreased the inhibition potential of andrographolide towards (R)‐fenoprofen metabolism (P < 0.001). Different from (R)‐fenoprofen, the addition of BSA significantly increased the inhibition potential of andrographolide towards the metabolism of (S)‐fenoprofen. BSA supplement also changed the inhibition kinetic type and parameter of andrographolide towards the metabolism of (S)‐fenoprofen. In conclusion, albumin supplement changes the metabolic behavior of fenoprofen enantiomers and the fenoprofen–andrographolide interaction. Chirality 27:436–440, 2015. © 2015 Wiley Periodicals, Inc.     

自杀行为的生物遗传因素研究

自杀是我国15-34岁人群首位重要的死亡原因。自杀行为的发生与生物学、心理学、社会学等多种因素有关。研究表明自杀行为确有一定的遗传学基础,近年来自杀行为的生物遗传因素研究发现5-HT系统相关基因、儿茶酚胺氧位甲基转移酶基因、精胺/精脒乙酰转移酶基因等候选基因单核甘酸多态性与自杀行为有明显关联。有学者认为,自杀行为的遗传学基础可能是附加于精神疾病的遗传或家庭环境诱导所致。本文就近年来国内外有关自杀的主要相关基因研究发现作一综述。     

细胞色素P450调节肝脏药物代谢的途径

大量研究认为细胞色素P450与药物性肝损伤的病理生理过程密切相关,对其在肝损伤的作用已成为当前研究的一个热点.主要介绍细胞色素P450与药物性肝损伤的相关研究进展.     

Evolution and diversity of the 2–oxoglutarate‐dependent dioxygenase superfamily in plants

The 2–oxoglutarate‐dependent dioxygenase (2OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation/hydroxylation reactions. Despite their biochemical significance in metabolism, a systematic analysis of plant 2OGDs remains to be accomplished. We present a phylogenetic classification of 479 2OGDs in six plant models, ranging from green algae to angiosperms. These were classified into three classes – DOXA, DOXB and DOXC – based on amino acid sequence similarity. The DOXA class includes plant homologs of Escherichia coli AlkB, which is a prototype of 2OGD involved in the oxidative demethylation of alkylated nucleic acids and histones. The DOXB class is conserved across all plant taxa and is involved in proline 4–hydroxylation in cell wall protein synthesis. The DOXC class is involved in specialized metabolism of various phytochemicals, including phytohormones and flavonoids. The vast majority of 2OGDs from land plants were classified into the DOXC class, but only seven from Chlamydomonas, suggesting that this class has diversified during land plant evolution. Phylogenetic analysis assigned DOXC‐class 2OGDs to 57 phylogenetic clades. 2OGD genes involved in gibberellin biosynthesis were conserved among vascular plants, and those involved in flavonoid and ethylene biosynthesis were shared among seed plants. Several angiosperm‐specific clades were found to be involved in various lineage‐specific specialized metabolisms, but 31 of the 57 DOXC‐class clades were only found in a single species. Therefore, the evolution and diversification of DOXC‐class 2OGDs is partly responsible for the diversity and complexity of specialized metabolites in land plants.     

snpqc – an R pipeline for quality control of Illumina SNP genotyping array data

In genome‐wide association studies, quality control (QC) of genotypes is important to avoid spurious results. It is also important to maintain long‐term data integrity, particularly in settings with ongoing genotyping (e.g. estimation of genomic breeding values). Here we discuss snpqc , a fully automated pipeline to perform QC analyses of Illumina SNP array data. It applies a wide range of common quality metrics with user‐defined filtering thresholds to generate a comprehensive QC report and a filtered dataset, including a genomic relationship matrix, ready for further downstream analyses which make it amenable for integration in high‐throughput environments. snpqc also builds a database to store genotypic, phenotypic and quality metrics to ensure data integrity and the option of integrating more samples from subsequent runs. The program is generic across species and array designs, providing a convenient interface between the genotyping laboratory and downstream genome‐wide association study or genomic prediction.     

Design,synthesis, and conformational studies of the hGM‐CSF derived peptide (13–27)–Gly–(75–87)

An analogue of the human granulocyte–macrophage colony‐stimulating factor (hGM‐CSF), hGM‐CSF(13–27)–Gly–(75–87) was synthesized by solid phase methodology. This analogue was designed to comprise helices A and C of the native growth factor, linked by a glycine bridge. Helices A and C form half of a four‐helix bundle motif in the crystal structure of the native factor and are involved in the interaction with α‐ and β‐chains of the heterodimeric receptor. A conformational analysis of the synthetic analogue by CD, two‐dimensional nmr spectroscopy, and molecular dynamics calculations is reported. The analogue is in a random structure in water and assumes a partially α‐helical conformation in a 1 : 1 trifluoroethanol/water mixture. The helix content in this medium is ∼ 70%. By 2D‐nmr spectroscopy, two helical segments were identified in the sequences corresponding to helices A and C. In addition to medium‐ and short‐range NOESY connectivities, a long‐range cross peak was found between the Cβ proton of Val¹⁶ and NH proton of His⁸⁷ (using the numbering of the native protein). Experimentally derived interproton distances were used as restraints in molecular dynamics calculations, utilizing the x‐ray coordinates as the initial structure. The final structure is characterized by two helical segments in close spatial proximity, connected by a loop region. This structure is similar to that of the corresponding domain in the x‐ray structure of the native growth factor in which helices A and C are oriented in an antiparallel fashion. The N‐terminal residues Gly–Pro of helix C are involved in an irregular turn connecting the two helical segments. As a consequence, helix C is appreciably shifted and slightly rotated with respect to helix A compared to the x‐ray structure of the native growth factor. These small differences in the topology of the two helices could explain the lower biological activity of this analogue with respect to that of the native growth factor. © 1999 John Wiley & Sons, Inc. Biopoly 50: 545–554, 1999     

The ‘making of’ the Mulligans Flat – Goorooyarroo experimental restoration project

What happens when park managers and ecological researchers join forces to build an evidence‐based approach to restoring a nature reserve? This project shows how a spirit of cooperation and inventiveness overcome a range of challenges at one of the National Capital region’s most valuable examples of critically endangered box‐gum grassy woodland.